low density lipoprotein receptor related-2
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast Population▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Overview
Single cell RNA-seq of pluripotent neoblasts and its early progeniesWe isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)Explore this single cell expression dataset with our NB Cluster Shiny App
Neoblast Population
Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Embryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30035485 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Homology
BLAST of low density lipoprotein receptor related-2 vs. TrEMBL
Match: I1ZIG1 (Low density lipoprotein receptor related-2 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1) HSP 1 Score: 390.193 bits (1001), Expect = 3.785e-133 Identity = 256/269 (95.17%), Postives = 256/269 (95.17%), Query Frame = 1 Query: 199 DRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGXXXXXXXXXXXXXXXXXXXXXXXTENKSSNTESKKFLXXXXXXXXXXXXXXLETDDCKTEKNECCATKMCC 1005 D KDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFD KGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTE DD CCIKICLETDDCKTEKNECCATKMCC Sbjct: 1 DGKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDEKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTEICCSS-----DDCCCIKICLETDDCKTEKNECCATKMCC 264 HSP 2 Score: 74.7146 bits (182), Expect = 1.379e-11 Identity = 76/186 (40.86%), Postives = 96/186 (51.61%), Query Frame = 1 Query: 187 HCVMDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEK----CQLKFCKTAICGKSDKCFGIKVCPDKEDGQ---NHCELKLCNPEICGKSDECCCITVC-----------KKENSGKFEE-------CCSIKVCLDKNDCKDEEDKIYQLKFC 669 HC + + C SD CC CK E S K +ECC I+VCLD+ND K++ QLKFCK ICGKSD+C IKVC +++D Q N C+ KLCNPEICGK +ECCC+ VC K EN E CC IK+CL+ +DCK E+++ K C Sbjct: 98 HCELKLCNPEICGKSDECCC-----ITVCKKENS---------------GKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTEICCSSDDCCCIKICLETDDCKTEKNECCATKMC 263
BLAST of low density lipoprotein receptor related-2 vs. Planmine SMEST
Match: SMESG000041448.1 (SMESG000041448.1) HSP 1 Score: 353.214 bits (905), Expect = 2.067e-122 Identity = 242/270 (89.63%), Postives = 242/270 (89.63%), Query Frame = 1 Query: 196 MDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGXXXXXXXXXXXXXXXXXXXXXXXTENKSSNTESKKFLXXXXXXXXXXXXXXLETDDCKTEKNECCATKMCC 1005 MD KDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFD KGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNP ENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTE SSDD CCIKICLETDDCKTEKNECCATKMCC Sbjct: 1 MDGKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDEKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNP-----------------ENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTEICC-----SSDDCCCIKICLETDDCKTEKNECCATKMCC 248
BLAST of low density lipoprotein receptor related-2 vs. Planmine SMEST
Match: SMESG000041448.1 (SMESG000041448.1) HSP 1 Score: 297.36 bits (760), Expect = 6.674e-101 Identity = 197/270 (72.96%), Postives = 202/270 (74.81%), Query Frame = 1 Query: 196 MDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGXXXXXXXXXXXXXXXXXXXXXXXTENKSSNTESKKFLXXXXXXXXXXXXXXLETDDCKTEKNECCATKMCC 1005 MD KDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFD KGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNP ENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGK +ECCC+KVCLE+KD +D + TENKSSNTE SSDD CCIKICLETDDCKTEKNECCATKMCC Sbjct: 1 MDGKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDEKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNP-----------------ENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKFEECCCVKVCLEKKDSKDLKDK-----------------------------------TENKSSNTEICC-----SSDDCCCIKICLETDDCKTEKNECCATKMCC 213
BLAST of low density lipoprotein receptor related-2 vs. Planmine SMEST
Match: SMESG000041448.1 (SMESG000041448.1) HSP 1 Score: 265.003 bits (676), Expect = 3.741e-88 Identity = 180/270 (66.67%), Postives = 191/270 (70.74%), Query Frame = 1 Query: 196 MDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGXXXXXXXXXXXXXXXXXXXXXXXTENKSSNTESKKFLXXXXXXXXXXXXXXLETDDCKTEKNECCATKMCC 1005 MD KDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFD KGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCC IKVCL++ DC+D ++ + K C EICGK +ECCC+KVCLE+KD +D + TENKSSNTE DD CCIKICLETDDCKTEKNECCATKMCC Sbjct: 1 MDGKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDEKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCC-----------------IKVCLERKDCQD-QNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDK-----------------------------------TENKSSNTEICCSS-----DDCCCIKICLETDDCKTEKNECCATKMCC 212
BLAST of low density lipoprotein receptor related-2 vs. Planmine SMEST
Match: SMESG000041448.1 (SMESG000041448.1) HSP 1 Score: 252.292 bits (643), Expect = 4.152e-83 Identity = 198/270 (73.33%), Postives = 202/270 (74.81%), Query Frame = 1 Query: 196 MDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQNHCELKLCNPEICGKSDECCCITVCKKENSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGXXXXXXXXXXXXXXXXXXXXXXXTENKSSNTESKKFLXXXXXXXXXXXXXXLETDDCKTEKNECCATKMCC 1005 MD KDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFD KGCAKSDECC GI+VC D+ D + C+LK C K NSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTE SSDD CCIKICLETDDCKTEKNECCATKMCC Sbjct: 1 MDGKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDEKGCAKSDECC--------------------------------GIRVCLDRNDRKEKCQLKFC-----------------KTANSGKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTEICC-----SSDDCCCIKICLETDDCKTEKNECCATKMCC 216
BLAST of low density lipoprotein receptor related-2 vs. Planmine SMEST
Match: SMESG000041448.1 (SMESG000041448.1) HSP 1 Score: 189.889 bits (481), Expect = 2.429e-59 Identity = 121/179 (67.60%), Postives = 134/179 (74.86%), Query Frame = 1 Query: 196 MDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDKCFGIKVCPDKEDGQ---NHCELKLCNPEICGKSDECCCITVC-----------KKENSGKFEE-------CCSIKVCLDKNDCKDEEDKIYQLKFC 669 MD KDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFD KGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSD+C IKVC +++D Q N C+ KLCNPEICGK +ECCC+ VC K EN E CC IK+CL+ +DCK E+++ K C Sbjct: 1 MDGKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDEKGCAKSDECCGIRVCLDRNDRKEKCQLKFCKTAICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTEICCSSDDCCCIKICLETDDCKTEKNECCATKMC 179 HSP 2 Score: 127.102 bits (318), Expect = 3.785e-35 Identity = 116/143 (81.12%), Postives = 121/143 (84.62%), Query Frame = 1 Query: 577 GKFEECCSIKVCLDKNDCKDEEDKIYQLKFCKCEICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGXXXXXXXXXXXXXXXXXXXXXXXTENKSSNTESKKFLXXXXXXXXXXXXXXLETDDCKTEKNECCATKMCC 1005 K +ECC I+VCLD+ND K++ QLKFCK ICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTE DD CCIKICLETDDCKTEKNECCATKMCC Sbjct: 47 AKSDECCGIRVCLDRNDRKEK----CQLKFCKTAICGKSDECCCIKVCLERKDCQDQNNTCKFKLCNPEICGKFEECCCVKVCLEKKDSKDLKDKTENKSSNTEICCSS-----DDCCCIKICLETDDCKTEKNECCATKMCC 180 The following BLAST results are available for this feature:
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of low density lipoprotein receptor related-2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 5
Analyses
This transcript is derived from or has results from the following analyses Cross References
External references for this transcript
Sequences
The following sequences are available for this feature:
transcript sequence >SMED30035485 ID=SMED30035485|Name=low density lipoprotein receptor related-2|organism=Schmidtea mediterranea sexual|type=transcript|length=1080bpback to top protein sequence of SMED30035485-orf-1 >SMED30035485-orf-1 ID=SMED30035485-orf-1|Name=SMED30035485-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=271bp MDRKDKSCCVSSDRKCCKDGETSGDCKDEQSVCANFSKMSFDGKGCAKSDback to top Annotated Terms
The following terms have been associated with this transcript:
|